Zinc in PDB 1ylo: Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T

The structure of Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T, PDB code: 1ylo was solved by B.P.Nocek, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.15
Space group	I 41
Cell size a, b, c (Å), α, β, γ (°)	161.827, 161.827, 228.574, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T (pdb code 1ylo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T, PDB code: 1ylo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in the Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1446 b:37.6 occ:0.80 OD1 A:ASP166 2.0 37.5 1.0 OD1 A:ASP221 2.0 41.6 1.0 NE2 A:HIS62 2.1 34.8 1.0 O A:HOH1448 2.4 45.6 1.0 CG A:ASP221 2.8 39.2 1.0 OD2 A:ASP221 2.9 44.7 1.0 CG A:ASP166 2.9 36.0 1.0 CE1 A:HIS62 3.0 34.7 1.0 OD2 A:ASP166 3.1 40.9 1.0 CD2 A:HIS62 3.2 35.7 1.0 ZN A:ZN1447 3.4 47.6 0.4 OE2 A:GLU199 3.8 48.4 1.0 OE2 A:GLU198 3.8 44.7 0.5 ND1 A:HIS62 4.2 34.9 1.0 CG A:HIS62 4.3 35.0 1.0 CB A:ASP166 4.3 31.9 1.0 CB A:ASP167 4.3 30.9 1.0 CB A:ASP221 4.3 37.1 1.0 CG A:ASP167 4.4 33.2 1.0 CD A:GLU199 4.5 47.0 1.0 O A:HOH1532 4.5 53.0 1.0 CD A:GLU198 4.5 44.6 0.5 OD2 A:ASP167 4.6 33.1 1.0 CG A:GLU198 4.6 42.3 0.5 CA A:ASP166 4.7 31.2 1.0 C A:ASP166 4.8 30.9 1.0 OD1 A:ASP167 4.8 31.8 1.0 N A:THR222 4.9 37.9 1.0 OE1 A:GLU199 4.9 47.5 1.0 CA A:ASP221 4.9 36.5 1.0 N A:ASP167 4.9 30.6 1.0 O A:THR222 5.0 38.5 1.0

Zinc binding site 2 out of 12 in the Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1447 b:47.6 occ:0.43 OE2 A:GLU199 2.0 48.4 1.0 OD2 A:ASP166 2.0 40.9 1.0 NE2 A:HIS308 2.1 40.7 1.0 O A:HOH1448 2.4 45.6 1.0 OE1 A:GLU199 2.7 47.5 1.0 CD A:GLU199 2.7 47.0 1.0 CE1 A:HIS308 2.9 40.6 1.0 CG A:ASP166 3.0 36.0 1.0 CD2 A:HIS308 3.2 37.9 1.0 OD1 A:ASP166 3.4 37.5 1.0 ZN A:ZN1446 3.4 37.6 0.8 O A:HOH1532 3.6 53.0 1.0 ND1 A:HIS308 4.0 38.3 1.0 CG A:GLU199 4.2 45.0 1.0 CB A:ASP166 4.2 31.9 1.0 CG A:HIS308 4.2 36.2 1.0 O A:HOH1472 4.3 29.6 1.0 CE1 A:HIS62 4.5 34.7 1.0 CG1 A:VAL66 4.5 30.9 1.0 NE2 A:HIS62 4.6 34.8 1.0 O A:HOH1531 4.6 44.0 1.0 O A:ASP166 4.9 30.5 1.0

Zinc binding site 3 out of 12 in the Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1546 b:36.7 occ:0.80 OD1 B:ASP166 2.0 37.8 1.0 OD1 B:ASP221 2.0 41.7 1.0 NE2 B:HIS62 2.1 34.5 1.0 O B:HOH1570 2.4 39.6 1.0 O B:HOH1605 2.4 52.2 1.0 CG B:ASP221 2.8 39.8 1.0 OD2 B:ASP221 2.9 44.5 1.0 CG B:ASP166 2.9 35.6 1.0 CE1 B:HIS62 3.0 34.0 1.0 OD2 B:ASP166 3.2 42.1 1.0 CD2 B:HIS62 3.2 34.7 1.0 ZN B:ZN1547 3.4 49.3 0.4 OE1 B:GLU198 3.8 44.1 0.5 OE2 B:GLU198 4.0 44.6 0.5 OE2 B:GLU199 4.0 49.9 1.0 CD B:GLU198 4.1 44.4 0.5 ND1 B:HIS62 4.2 32.8 1.0 CG B:HIS62 4.3 33.0 1.0 CB B:ASP221 4.3 37.6 1.0 CB B:ASP166 4.4 32.0 1.0 CB B:ASP167 4.4 30.8 1.0 CG B:ASP167 4.5 32.7 1.0 CD B:GLU199 4.5 47.9 1.0 O B:HOH1622 4.6 41.2 1.0 OD2 B:ASP167 4.7 33.7 1.0 OE1 B:GLU199 4.8 48.4 1.0 CA B:ASP166 4.8 31.5 1.0 C B:ASP166 4.9 31.3 1.0 OD1 B:ASP167 4.9 31.5 1.0 CA B:ASP221 4.9 36.9 1.0 N B:THR222 5.0 37.9 1.0

Zinc binding site 4 out of 12 in the Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1547 b:49.3 occ:0.43 OE2 B:GLU199 2.0 49.9 1.0 OD2 B:ASP166 2.0 42.1 1.0 NE2 B:HIS308 2.1 42.6 1.0 O B:HOH1570 2.4 39.6 1.0 OE1 B:GLU199 2.6 48.4 1.0 CD B:GLU199 2.6 47.9 1.0 CG B:ASP166 2.9 35.6 1.0 CE1 B:HIS308 2.9 41.9 1.0 CD2 B:HIS308 3.1 40.1 1.0 OD1 B:ASP166 3.3 37.8 1.0 ZN B:ZN1546 3.4 36.7 0.8 O B:HOH1605 3.7 52.2 1.0 CB B:ASP166 4.0 32.0 1.0 ND1 B:HIS308 4.1 40.5 1.0 CG B:GLU199 4.1 45.8 1.0 CG B:HIS308 4.2 37.7 1.0 O B:HOH1584 4.2 33.1 1.0 CE1 B:HIS62 4.4 34.0 1.0 CG1 B:VAL66 4.4 29.3 1.0 OE1 B:GLU198 4.5 44.1 0.5 NE2 B:HIS62 4.5 34.5 1.0 O B:HOH1593 4.6 37.9 1.0 O B:ASP166 4.8 31.4 1.0

Zinc binding site 5 out of 12 in the Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1646 b:38.0 occ:0.80 OD1 C:ASP166 2.0 39.1 1.0 OD1 C:ASP221 2.0 41.0 1.0 NE2 C:HIS62 2.1 35.2 1.0 O C:HOH1690 2.4 45.8 1.0 CG C:ASP221 2.8 40.0 1.0 OD2 C:ASP221 2.8 45.3 1.0 CG C:ASP166 3.0 35.2 1.0 CE1 C:HIS62 3.0 35.1 1.0 CD2 C:HIS62 3.2 35.2 1.0 OD2 C:ASP166 3.3 41.1 1.0 ZN C:ZN1647 3.5 47.7 0.4 OE2 C:GLU199 3.8 49.1 1.0 OE2 C:GLU198 3.9 45.0 0.5 OE1 C:GLU198 4.0 44.7 0.5 CD C:GLU198 4.1 44.7 0.5 ND1 C:HIS62 4.1 35.1 1.0 CB C:ASP167 4.2 30.3 1.0 CG C:ASP167 4.2 32.0 1.0 CB C:ASP221 4.3 37.9 1.0 CG C:HIS62 4.3 33.6 1.0 CB C:ASP166 4.4 31.2 1.0 O C:HOH1708 4.4 46.0 1.0 OD2 C:ASP167 4.4 33.7 1.0 CD C:GLU199 4.6 48.8 1.0 OD1 C:ASP167 4.7 31.1 1.0 CA C:ASP166 4.7 30.4 1.0 C C:ASP166 4.8 30.0 1.0 CA C:ASP221 4.9 37.4 1.0 CA C:ASP167 4.9 30.1 1.0 N C:ASP167 4.9 29.9 1.0 N C:THR222 4.9 38.4 1.0 OE1 C:GLU199 5.0 49.7 1.0

Zinc binding site 6 out of 12 in the Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1647 b:47.7 occ:0.43 OE2 C:GLU199 2.0 49.1 1.0 OD2 C:ASP166 2.0 41.1 1.0 NE2 C:HIS308 2.1 41.4 1.0 O C:HOH1690 2.4 45.8 1.0 OE1 C:GLU199 2.6 49.7 1.0 CD C:GLU199 2.7 48.8 1.0 CE1 C:HIS308 2.8 41.5 1.0 CG C:ASP166 3.0 35.2 1.0 CD2 C:HIS308 3.2 40.3 1.0 OD1 C:ASP166 3.4 39.1 1.0 ZN C:ZN1646 3.5 38.0 0.8 ND1 C:HIS308 4.0 40.6 1.0 CG C:GLU199 4.2 47.3 1.0 CB C:ASP166 4.2 31.2 1.0 CG C:HIS308 4.2 38.0 1.0 O C:HOH1672 4.4 30.2 1.0 OE2 C:GLU198 4.4 45.0 0.5 CG1 C:VAL66 4.6 30.1 1.0 CE1 C:HIS62 4.6 35.1 1.0 O C:HOH1732 4.6 38.3 1.0 NE2 C:HIS62 4.6 35.2 1.0

Zinc binding site 7 out of 12 in the Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1746 b:37.4 occ:0.80 OD1 D:ASP166 2.0 38.6 1.0 OD1 D:ASP221 2.0 39.2 1.0 O D:HOH1820 2.3 50.8 1.0 NE2 D:HIS62 2.4 34.4 1.0 OD2 D:ASP221 2.7 43.0 1.0 CG D:ASP221 2.7 37.3 1.0 CG D:ASP166 2.9 34.7 1.0 OD2 D:ASP166 3.2 40.0 1.0 CE1 D:HIS62 3.4 33.5 1.0 CD2 D:HIS62 3.4 34.2 1.0 ZN D:ZN1747 3.4 48.1 0.4 OE2 D:GLU198 3.8 45.5 0.5 OE2 D:GLU199 3.9 50.5 1.0 CB D:ASP221 4.3 35.6 1.0 CB D:ASP167 4.3 30.0 1.0 CB D:ASP166 4.3 31.1 1.0 CG D:ASP167 4.4 32.0 1.0 ND1 D:HIS62 4.5 33.0 1.0 CD D:GLU198 4.5 45.5 0.5 CG D:GLU198 4.5 43.7 0.5 CG D:HIS62 4.6 33.2 1.0 OD2 D:ASP167 4.6 33.4 1.0 CD D:GLU199 4.6 49.5 1.0 OD2 D:ASP284 4.7 63.2 1.0 OD1 D:ASP167 4.8 31.1 1.0 CA D:ASP166 4.8 30.5 1.0 C D:ASP166 4.9 30.3 1.0 CA D:ASP221 4.9 35.3 1.0 N D:THR222 5.0 36.7 1.0 OE1 D:GLU199 5.0 49.8 1.0

Zinc binding site 8 out of 12 in the Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1747 b:48.1 occ:0.43 OE2 D:GLU199 2.0 50.5 1.0 OD2 D:ASP166 2.0 40.0 1.0 NE2 D:HIS308 2.1 40.0 1.0 O D:HOH1820 2.2 50.8 1.0 OE1 D:GLU199 2.7 49.8 1.0 CD D:GLU199 2.7 49.5 1.0 CE1 D:HIS308 2.8 39.6 1.0 CG D:ASP166 2.9 34.7 1.0 CD2 D:HIS308 3.2 37.7 1.0 OD1 D:ASP166 3.4 38.6 1.0 ZN D:ZN1746 3.4 37.4 0.8 ND1 D:HIS308 4.0 38.0 1.0 CG D:GLU199 4.2 47.3 1.0 O D:HOH1766 4.2 32.8 1.0 CB D:ASP166 4.2 31.1 1.0 CG D:HIS308 4.2 36.1 1.0 CG1 D:VAL66 4.4 29.9 1.0 O D:HOH1770 4.6 36.2 1.0 NE2 D:HIS62 4.6 34.4 1.0 CE1 D:HIS62 4.7 33.5 1.0 O D:ASP166 5.0 30.6 1.0 OE2 D:GLU198 5.0 45.5 0.5

Zinc binding site 9 out of 12 in the Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1846 b:36.2 occ:0.80 OD1 E:ASP166 2.0 37.1 1.0 OD1 E:ASP221 2.0 41.3 1.0 NE2 E:HIS62 2.1 33.4 1.0 O E:HOH1852 2.5 42.7 1.0 O E:HOH1931 2.7 58.5 1.0 CG E:ASP221 2.8 39.5 1.0 OD2 E:ASP221 2.9 44.9 1.0 CG E:ASP166 3.0 35.4 1.0 CE1 E:HIS62 3.0 32.8 1.0 CD2 E:HIS62 3.2 32.4 1.0 OD2 E:ASP166 3.2 41.4 1.0 ZN E:ZN1847 3.4 49.1 0.4 OE2 E:GLU198 3.7 46.7 0.5 OE2 E:GLU199 3.8 50.4 1.0 ND1 E:HIS62 4.2 32.4 1.0 O E:HOH1907 4.3 46.4 1.0 CB E:ASP167 4.3 30.6 1.0 CG E:HIS62 4.3 33.0 1.0 CB E:ASP221 4.3 36.9 1.0 CB E:ASP166 4.4 32.0 1.0 CG E:ASP167 4.4 32.2 1.0 CD E:GLU198 4.5 45.7 0.5 CD E:GLU199 4.5 49.5 1.0 OD2 E:ASP167 4.6 33.3 1.0 CG E:GLU198 4.6 43.6 0.5 CA E:ASP166 4.8 31.2 1.0 C E:ASP166 4.8 31.1 1.0 OE1 E:GLU199 4.9 50.3 1.0 OD1 E:ASP167 4.9 31.6 1.0 CA E:ASP221 4.9 36.5 1.0

Zinc binding site 10 out of 12 in the Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Protein of Unknown Function (Possible Aminopeptidase) S2589 From Shigella Flexneri 2A Str. 2457T within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1847 b:49.1 occ:0.43 OE2 E:GLU199 2.0 50.4 1.0 OD2 E:ASP166 2.0 41.4 1.0 NE2 E:HIS308 2.1 42.3 1.0 O E:HOH1852 2.2 42.7 1.0 OE1 E:GLU199 2.6 50.3 1.0 CD E:GLU199 2.6 49.5 1.0 CE1 E:HIS308 2.7 41.5 1.0 CG E:ASP166 3.0 35.4 1.0 CD2 E:HIS308 3.3 39.4 1.0 OD1 E:ASP166 3.4 37.1 1.0 ZN E:ZN1846 3.4 36.2 0.8 O E:HOH1931 3.7 58.5 1.0 ND1 E:HIS308 3.9 40.6 1.0 CG E:GLU199 4.1 47.0 1.0 CB E:ASP166 4.2 32.0 1.0 CG E:HIS308 4.2 37.8 1.0 CE1 E:HIS62 4.4 32.8 1.0 O E:HOH1871 4.5 30.5 1.0 CG1 E:VAL66 4.5 30.5 1.0 NE2 E:HIS62 4.6 33.4 1.0 O E:HOH1884 4.6 32.4 1.0

B.P.Nocek, A.Binkowski, H.Li, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg). Crystal Structure of Hypothetical Protein From Shigella Flexneri 2A. To Be Published.